Type II transmembrane domain hydrophobicity dictates the cotranslational dependence for inversion.
Bottom Line: This places stringent hydrophobicity requirements on transmembrane domains (TMDs) from single-spanning membrane proteins.On examining the single-spanning influenza A membrane proteins, we found that the strict hydrophobicity requirement applies to the N(out)-C(in) HA and M2 TMDs but not the N(in)-C(out) TMDs from the type II membrane protein neuraminidase (NA).To investigate this discrepancy, we analyzed NA TMDs of varying hydrophobicity, followed by increasing polypeptide lengths, in mammalian cells and ER microsomes.
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Mentions: The analysis of protein sequence homology, property, and structural conservation has proved extremely useful in identifying protein topology and localization, functional domains, and the existence of certain cellular machinery (von Heijne, 2006; Daniels et al., 2010). However, the limited number of homologous sequences for human single-spanning membrane protein has hindered these approaches. Therefore we used the extensive human influenza A virus (IAV) sequence database to perform a comparative analysis of the TMD characteristics from natural single-spanning membrane proteins with Nout-Cin (HA and M2) and Nin-Cout (NA) orientations (Figure 1A).